More on 2009 Mac Pro Northbridge Heatsink Retainer Repairs:
Another reader report on repairing broken plastic NB heatsink retainers.
(FYI: If buying one of these CPU boards, remember that the SMC version of the CPU board and main board must match for proper function. The 2010-2012 Mac Pro CPU boards have a different (later) SMC version than the 2009 Mac Pro boards. I don't know of any 'unofficial' SMC firmware update for that like there was for the Mac Pro 4,1 to 5,1 EFI firmware.)

"2009 Mac Pro - Missing Northbridge retainer causes failure to boot
A longtime reader checking in again. I've dropped my Mini's in favor of Apple TV as a set top box and jumped into Mac Pro 2009 models as play toys... I did a few hex-core upgrades and feeling full of myself, I bought two "dead" CPU boards off Ebay. It seems that sometimes the failure is the processor and I had a few laying around by now.

(** For anyone buying a used CPU board for a 2009 or 2010-2012 Mac Pro, the SMC firmware version in the CPU board has to match the motherboard/backplane SMC version. (Have the seller confirm (in writing) it's from a Mac Pro that matches your series.) There is a later SMC version in post-2009 Mac Pros but can't recall the number now. Apple's doc on EFI/SMC updates to date doesn't list any SMC version or update for the 2009 or 2010-2012 Mac Pros. They only list a version if there was a publicly released update so that doesn't mean they were all the same. If you have no other way, the 2010-2012 Mac Pros shipped with CPUs that have an integrated heat spreader (metal lid) - the 2009 Mac Pro CPUs didn't.)

They lit the CPU LED immediately at startup and failed to boot (no startup chime, etc.). The OVTMP CPUA LED lit after a few moments. Swapped CPUs and still had failures. While swapping, I noticed a missing Northbridge heat sink retainer on each board. Nothing in the literature (repair forums, Apple Service Manual, etc.) about this type of failure from a missing retainer and I presumed I would have a bit of time to see a temperature problem manifest itself before it caused trouble. Certainly nothing immediately after I pushed the power button.

Having two good retainers between the two boards, I made one whole. Voila, a working processor board. It's cranking at 100% CPU utilization now (distributed.net) and maintaining 53°C/43°C on the Northbridge chip/heatsink sensors (per Hardware Monitor).

I don't know how many of these are out there (with only broken retainer problems), but I'm betting more than the two I have. (Sellers of 'bad' boards may check for broken retainers which I suspect will be more common over time as the plastic ages and breaks from stress.)

One still to go, my other upgrades all have good retainers and I have no stock of screws to do the second, until tomorrow of course.

(he later wrote)
Day two, still lucky. Second 'dead' processor board now breathing and holding steady at 63°C/53°C while at 100% cpu utilization. About 50 cents worth of nylon screws, washers, and nuts.
Just about ready for the dual hex upgrade ...
-Dana"